/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_RMDUP_BAM_WORKER_H_
#define _U2_RMDUP_BAM_WORKER_H_

#include <U2Core/GUrl.h>

#include <U2Lang/LocalDomain.h>
#include <U2Lang/WorkflowUtils.h>

namespace U2 {
namespace LocalWorkflow {

class RmdupBamPrompter;
typedef PrompterBase<RmdupBamPrompter> RmdupBamBase;

class RmdupBamPrompter : public RmdupBamBase {
    Q_OBJECT
public:
    RmdupBamPrompter(Actor *p = 0)
        : RmdupBamBase(p) {
    }

protected:
    QString composeRichDoc();
};    //RmdupBamPrompter

class RmdupBamWorker : public BaseWorker {
    Q_OBJECT
public:
    RmdupBamWorker(Actor *a);
    void init();
    Task *tick();
    void cleanup();

private:
    IntegralBus *inputUrlPort;
    IntegralBus *outputUrlPort;
    QStringList outUrls;
public slots:
    void sl_taskFinished(Task *task);

private:
    QString takeUrl();
    QString getTargetName(const QString &fileUrl, const QString &outDir);
    void sendResult(const QString &url);
};    //RmdupBamWorker

class RmdupBamWorkerFactory : public DomainFactory {
    static const QString ACTOR_ID;

public:
    static void init();
    RmdupBamWorkerFactory()
        : DomainFactory(ACTOR_ID) {
    }
    Worker *createWorker(Actor *a) {
        return new RmdupBamWorker(a);
    }
};    //RmdupBamWorkerFactory

class BamRmdupSetting {
public:
    BamRmdupSetting()
        : outDir(""), outName(""), inputUrl(""), removeSingleEnd(false), treatReads(false) {
    }

    QString outDir;
    QString outName;
    QString inputUrl;
    bool removeSingleEnd;
    bool treatReads;

    QStringList getSamtoolsArguments() const;
};

class SamtoolsRmdupTask : public ExternalToolSupportTask {
    Q_OBJECT
public:
    SamtoolsRmdupTask(const BamRmdupSetting &settings);

    void prepare();
    void run();

    QString getResult() {
        return resultUrl;
    }

private:
    void start(const ProcessRun &pRun, const QString &toolName);
    void checkExitCode(QProcess *process, const QString &toolName);

private:
    BamRmdupSetting settings;
    QString resultUrl;

    static const QString SAMTOOLS_ID;    // this constant is taken from the appropriate file in external_tool_support plugin
};

}    // namespace LocalWorkflow
}    // namespace U2

#endif    //_U2_REMDUP_BAM_WORKER_H_
